[2023-06-13 05:12:33,618] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:12:33,622] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:12:33,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg202b22ee-0350-40e8-8656-9420a5444a19/dqc_reference
[2023-06-13 05:12:35,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:12:35,690] [INFO] Task started: Prodigal
[2023-06-13 05:12:35,690] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb9602ff-4023-4cbd-8b54-12336b5897aa/GCA_022790875.1_ASM2279087v1_genomic.fna.gz | prodigal -d GCA_022790875.1_ASM2279087v1_genomic.fna/cds.fna -a GCA_022790875.1_ASM2279087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:12:42,234] [INFO] Task succeeded: Prodigal
[2023-06-13 05:12:42,235] [INFO] Task started: HMMsearch
[2023-06-13 05:12:42,235] [INFO] Running command: hmmsearch --tblout GCA_022790875.1_ASM2279087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg202b22ee-0350-40e8-8656-9420a5444a19/dqc_reference/reference_markers.hmm GCA_022790875.1_ASM2279087v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:12:42,407] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:12:42,408] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfb9602ff-4023-4cbd-8b54-12336b5897aa/GCA_022790875.1_ASM2279087v1_genomic.fna.gz]
[2023-06-13 05:12:42,437] [INFO] Query marker FASTA was written to GCA_022790875.1_ASM2279087v1_genomic.fna/markers.fasta
[2023-06-13 05:12:42,437] [INFO] Task started: Blastn
[2023-06-13 05:12:42,438] [INFO] Running command: blastn -query GCA_022790875.1_ASM2279087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg202b22ee-0350-40e8-8656-9420a5444a19/dqc_reference/reference_markers.fasta -out GCA_022790875.1_ASM2279087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:12:42,958] [INFO] Task succeeded: Blastn
[2023-06-13 05:12:42,961] [INFO] Selected 20 target genomes.
[2023-06-13 05:12:42,962] [INFO] Target genome list was writen to GCA_022790875.1_ASM2279087v1_genomic.fna/target_genomes.txt
[2023-06-13 05:12:42,973] [INFO] Task started: fastANI
[2023-06-13 05:12:42,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb9602ff-4023-4cbd-8b54-12336b5897aa/GCA_022790875.1_ASM2279087v1_genomic.fna.gz --refList GCA_022790875.1_ASM2279087v1_genomic.fna/target_genomes.txt --output GCA_022790875.1_ASM2279087v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:12:55,177] [INFO] Task succeeded: fastANI
[2023-06-13 05:12:55,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg202b22ee-0350-40e8-8656-9420a5444a19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:12:55,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg202b22ee-0350-40e8-8656-9420a5444a19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:12:55,182] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:12:55,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 05:12:55,182] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	75.9315	52	818	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	75.8829	54	818	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 05:12:55,184] [INFO] DFAST Taxonomy check result was written to GCA_022790875.1_ASM2279087v1_genomic.fna/tc_result.tsv
[2023-06-13 05:12:55,184] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:12:55,185] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:12:55,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg202b22ee-0350-40e8-8656-9420a5444a19/dqc_reference/checkm_data
[2023-06-13 05:12:55,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:12:55,212] [INFO] Task started: CheckM
[2023-06-13 05:12:55,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022790875.1_ASM2279087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022790875.1_ASM2279087v1_genomic.fna/checkm_input GCA_022790875.1_ASM2279087v1_genomic.fna/checkm_result
[2023-06-13 05:13:20,837] [INFO] Task succeeded: CheckM
[2023-06-13 05:13:20,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:13:20,852] [INFO] ===== Completeness check finished =====
[2023-06-13 05:13:20,852] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:13:20,853] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022790875.1_ASM2279087v1_genomic.fna/markers.fasta)
[2023-06-13 05:13:20,853] [INFO] Task started: Blastn
[2023-06-13 05:13:20,853] [INFO] Running command: blastn -query GCA_022790875.1_ASM2279087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg202b22ee-0350-40e8-8656-9420a5444a19/dqc_reference/reference_markers_gtdb.fasta -out GCA_022790875.1_ASM2279087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:13:21,312] [INFO] Task succeeded: Blastn
[2023-06-13 05:13:21,316] [INFO] Selected 14 target genomes.
[2023-06-13 05:13:21,316] [INFO] Target genome list was writen to GCA_022790875.1_ASM2279087v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:13:21,329] [INFO] Task started: fastANI
[2023-06-13 05:13:21,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb9602ff-4023-4cbd-8b54-12336b5897aa/GCA_022790875.1_ASM2279087v1_genomic.fna.gz --refList GCA_022790875.1_ASM2279087v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022790875.1_ASM2279087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:13:29,112] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:29,119] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:13:29,119] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_910588815.1	s__Paralachnospira sp910588815	99.9087	736	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910587905.1	s__Paralachnospira sp910587905	82.753	481	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904420245.1	s__Paralachnospira avium	77.6262	204	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904379015.1	s__Paralachnospira caecorum	77.519	179	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	99.98	99.98	0.92	0.92	2	-
GCA_910577765.1	s__Ventrimonas sp910577765	76.2465	50	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160755.1	s__Lachnoclostridium_A sp002160755	76.1287	74	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-13 05:13:29,121] [INFO] GTDB search result was written to GCA_022790875.1_ASM2279087v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:13:29,121] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:13:29,124] [INFO] DFAST_QC result json was written to GCA_022790875.1_ASM2279087v1_genomic.fna/dqc_result.json
[2023-06-13 05:13:29,124] [INFO] DFAST_QC completed!
[2023-06-13 05:13:29,124] [INFO] Total running time: 0h0m56s